Multiple sequence alignment - TraesCS1D01G438500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G438500 chr1D 100.000 3006 0 0 1 3006 485419437 485422442 0.000000e+00 5552
1 TraesCS1D01G438500 chr1D 82.239 259 42 3 2343 2598 119005562 119005819 1.400000e-53 220
2 TraesCS1D01G438500 chr1D 81.579 152 21 5 488 637 389330472 389330618 5.260000e-23 119
3 TraesCS1D01G438500 chr1A 90.592 1807 107 19 1214 3004 582642419 582644178 0.000000e+00 2337
4 TraesCS1D01G438500 chr1A 91.102 472 20 11 781 1231 582641924 582642394 1.180000e-173 619
5 TraesCS1D01G438500 chr1A 86.667 375 26 4 13 383 582641067 582641421 7.810000e-106 394
6 TraesCS1D01G438500 chr1A 84.916 179 26 1 2125 2302 500348145 500347967 2.380000e-41 180
7 TraesCS1D01G438500 chr1B 91.892 1221 40 25 781 1977 675725994 675727179 0.000000e+00 1652
8 TraesCS1D01G438500 chr1B 84.019 1045 107 23 1968 3006 675727242 675728232 0.000000e+00 950
9 TraesCS1D01G438500 chr1B 85.219 663 77 9 1 653 675725147 675725798 0.000000e+00 662
10 TraesCS1D01G438500 chr1B 83.444 151 22 3 489 638 551030156 551030304 1.450000e-28 137
11 TraesCS1D01G438500 chr5D 75.286 700 130 21 2341 3004 565507272 565507964 8.150000e-76 294
12 TraesCS1D01G438500 chr3A 80.663 362 54 14 2341 2689 651652073 651652431 1.780000e-67 267
13 TraesCS1D01G438500 chr7D 75.214 585 112 20 2302 2873 136942786 136943350 2.310000e-61 246
14 TraesCS1D01G438500 chr7D 80.272 147 24 5 488 633 219632190 219632048 4.100000e-19 106
15 TraesCS1D01G438500 chr7D 79.870 154 24 7 487 638 521901479 521901331 4.100000e-19 106
16 TraesCS1D01G438500 chr3D 81.250 304 45 10 2302 2598 516674531 516674829 5.010000e-58 235
17 TraesCS1D01G438500 chr3D 82.911 158 26 1 2127 2283 383982715 383982872 1.120000e-29 141
18 TraesCS1D01G438500 chr3B 80.139 287 54 3 2341 2626 680629408 680629124 8.440000e-51 211
19 TraesCS1D01G438500 chr3B 83.673 196 31 1 2110 2304 775739214 775739409 1.840000e-42 183
20 TraesCS1D01G438500 chr6A 83.333 222 37 0 2357 2578 191273257 191273478 3.930000e-49 206
21 TraesCS1D01G438500 chr6A 79.006 181 37 1 2125 2304 369531869 369531689 4.070000e-24 122
22 TraesCS1D01G438500 chr2D 82.386 176 30 1 2130 2304 480103459 480103634 5.190000e-33 152
23 TraesCS1D01G438500 chr2A 78.302 212 41 4 2110 2317 408813414 408813624 6.760000e-27 132
24 TraesCS1D01G438500 chr2A 80.982 163 26 5 2125 2285 622289963 622290122 1.130000e-24 124
25 TraesCS1D01G438500 chr5B 83.571 140 17 4 501 638 694308160 694308295 3.150000e-25 126
26 TraesCS1D01G438500 chr6B 75.290 259 54 8 2717 2972 689915913 689915662 6.810000e-22 115
27 TraesCS1D01G438500 chr4A 80.795 151 25 3 489 637 649346755 649346607 6.810000e-22 115
28 TraesCS1D01G438500 chr5A 81.159 138 23 3 502 638 453532589 453532724 1.140000e-19 108
29 TraesCS1D01G438500 chr7A 78.750 160 25 8 482 637 244666639 244666793 6.860000e-17 99


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G438500 chr1D 485419437 485422442 3005 False 5552.000000 5552 100.000000 1 3006 1 chr1D.!!$F3 3005
1 TraesCS1D01G438500 chr1A 582641067 582644178 3111 False 1116.666667 2337 89.453667 13 3004 3 chr1A.!!$F1 2991
2 TraesCS1D01G438500 chr1B 675725147 675728232 3085 False 1088.000000 1652 87.043333 1 3006 3 chr1B.!!$F2 3005
3 TraesCS1D01G438500 chr5D 565507272 565507964 692 False 294.000000 294 75.286000 2341 3004 1 chr5D.!!$F1 663
4 TraesCS1D01G438500 chr7D 136942786 136943350 564 False 246.000000 246 75.214000 2302 2873 1 chr7D.!!$F1 571

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
703 780 0.040425 AAAACATCAACCGTCGCAGC 60.040 50.0 0.0 0.0 0.00 5.25 F
738 815 0.462047 ATCGAAGCGATCCAACCCAC 60.462 55.0 0.0 0.0 43.45 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 2253 0.236187 CCGGAAACAATCGCGTCAAA 59.764 50.0 5.77 0.0 0.00 2.69 R
2494 2784 0.599558 TACGGGAGGACGAGTTGTTG 59.400 55.0 0.00 0.0 37.61 3.33 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 2.380590 AGTGAACTGGTAGAGAGACCCT 59.619 50.000 0.00 0.00 38.89 4.34
52 53 2.517998 ACTGGTAGAGAGACCCTCAC 57.482 55.000 0.00 0.00 44.40 3.51
53 54 1.711375 ACTGGTAGAGAGACCCTCACA 59.289 52.381 0.00 0.00 44.40 3.58
54 55 2.110188 ACTGGTAGAGAGACCCTCACAA 59.890 50.000 0.00 0.00 44.40 3.33
55 56 2.494073 CTGGTAGAGAGACCCTCACAAC 59.506 54.545 0.00 0.00 44.40 3.32
56 57 2.158370 TGGTAGAGAGACCCTCACAACA 60.158 50.000 0.00 0.00 44.40 3.33
57 58 3.100671 GGTAGAGAGACCCTCACAACAT 58.899 50.000 0.00 0.00 44.40 2.71
58 59 3.515901 GGTAGAGAGACCCTCACAACATT 59.484 47.826 0.00 0.00 44.40 2.71
64 65 2.040412 AGACCCTCACAACATTCCCTTC 59.960 50.000 0.00 0.00 0.00 3.46
189 192 6.753107 AAAGGTGTATGTTTATAGGCACAC 57.247 37.500 0.00 0.00 36.43 3.82
193 196 7.745717 AGGTGTATGTTTATAGGCACACATAT 58.254 34.615 5.19 0.00 38.37 1.78
207 210 5.221461 GGCACACATATAGTACTAGGTTGCT 60.221 44.000 21.35 7.47 0.00 3.91
216 219 0.107654 ACTAGGTTGCTCCGATTGCC 60.108 55.000 0.00 0.00 41.99 4.52
228 231 1.314534 CGATTGCCATGCCACTTGGA 61.315 55.000 0.00 0.00 36.26 3.53
237 240 3.077907 CCACTTGGATCCCACCGT 58.922 61.111 9.90 0.00 37.39 4.83
274 277 0.250858 CACCCTCATGCTTCCACACA 60.251 55.000 0.00 0.00 0.00 3.72
316 319 1.763545 GATAGTGGACCTCTCCCAACC 59.236 57.143 0.00 0.00 35.34 3.77
470 512 8.192110 TCCTAACAAATGTGTCTTTACAAAACC 58.808 33.333 0.00 0.00 36.80 3.27
476 518 5.821516 TGTGTCTTTACAAAACCGAACAT 57.178 34.783 0.00 0.00 37.36 2.71
488 530 1.426621 CGAACATGCGCATTGCTCT 59.573 52.632 22.81 2.92 46.63 4.09
538 584 9.264653 TCTATTCATCATCTATCAAGGCAGTAT 57.735 33.333 0.00 0.00 0.00 2.12
550 596 3.275617 AGGCAGTATAATGAACGCCAA 57.724 42.857 3.96 0.00 38.29 4.52
567 613 8.138712 TGAACGCCAAAAGTAACTAAAAATCAT 58.861 29.630 0.00 0.00 0.00 2.45
586 632 8.674925 AAATCATATCCAAATTCATAGGCCAT 57.325 30.769 5.01 0.00 0.00 4.40
587 633 7.655521 ATCATATCCAAATTCATAGGCCATG 57.344 36.000 5.01 7.20 35.81 3.66
599 645 1.878522 GGCCATGTAGCGACGACTG 60.879 63.158 0.00 0.00 0.00 3.51
621 667 2.317609 GCACTGAAGCGAGCCGAAA 61.318 57.895 0.00 0.00 0.00 3.46
648 695 1.153765 CGCCATCAAGCAGAGTCGA 60.154 57.895 0.00 0.00 0.00 4.20
653 700 2.670414 CCATCAAGCAGAGTCGAAGAAC 59.330 50.000 0.00 0.00 39.69 3.01
654 701 3.583806 CATCAAGCAGAGTCGAAGAACT 58.416 45.455 0.00 0.00 39.69 3.01
655 702 3.018598 TCAAGCAGAGTCGAAGAACTG 57.981 47.619 0.00 0.00 42.79 3.16
657 704 2.430546 AGCAGAGTCGAAGAACTGTG 57.569 50.000 0.00 0.00 42.24 3.66
674 751 2.975489 CTGTGGTTAGGCCTCATAGGAT 59.025 50.000 9.68 0.00 39.69 3.24
685 762 0.744281 TCATAGGATCAGCGCACGAA 59.256 50.000 11.47 0.00 0.00 3.85
701 778 0.233590 CGAAAACATCAACCGTCGCA 59.766 50.000 0.00 0.00 0.00 5.10
703 780 0.040425 AAAACATCAACCGTCGCAGC 60.040 50.000 0.00 0.00 0.00 5.25
707 784 1.005037 ATCAACCGTCGCAGCTGAA 60.005 52.632 20.43 0.54 0.00 3.02
710 787 1.016130 CAACCGTCGCAGCTGAAGAT 61.016 55.000 20.43 0.00 0.00 2.40
736 813 4.857251 ATCGAAGCGATCCAACCC 57.143 55.556 0.00 0.00 43.45 4.11
737 814 1.904771 ATCGAAGCGATCCAACCCA 59.095 52.632 0.00 0.00 43.45 4.51
738 815 0.462047 ATCGAAGCGATCCAACCCAC 60.462 55.000 0.00 0.00 43.45 4.61
765 863 1.047034 GGGTGACGGGCCTACACTAT 61.047 60.000 22.30 0.00 35.28 2.12
794 909 5.413309 TTTGACCCTTCTTTTTGCAGAAA 57.587 34.783 2.07 2.07 32.24 2.52
797 912 4.466015 TGACCCTTCTTTTTGCAGAAACTT 59.534 37.500 0.00 0.00 32.24 2.66
821 936 1.255882 TAACATGCTGCCCCACAAAG 58.744 50.000 0.00 0.00 0.00 2.77
871 987 1.267121 TCTCAAGGTGGAGTGGCTAC 58.733 55.000 0.00 0.00 36.30 3.58
946 1071 3.165875 TGAGAATTCCGAGGACTTGACT 58.834 45.455 0.65 0.00 0.00 3.41
1070 1207 4.012374 TCCAGCTTTCCTTCACATGAATC 58.988 43.478 0.00 0.00 33.01 2.52
1103 1243 2.638330 TATTGGTAGCTGGCGCGGTC 62.638 60.000 8.83 0.00 42.32 4.79
1111 1251 2.954753 CTGGCGCGGTCAGTCAAAC 61.955 63.158 8.83 0.00 29.72 2.93
1406 1594 1.292941 CCTCCTCCTCCTCCTCCTCA 61.293 65.000 0.00 0.00 0.00 3.86
1407 1595 0.859760 CTCCTCCTCCTCCTCCTCAT 59.140 60.000 0.00 0.00 0.00 2.90
1408 1596 0.856982 TCCTCCTCCTCCTCCTCATC 59.143 60.000 0.00 0.00 0.00 2.92
1792 1991 3.545873 CGTCGATCTGCTTCTTCTTCTTC 59.454 47.826 0.00 0.00 0.00 2.87
1793 1992 4.674101 CGTCGATCTGCTTCTTCTTCTTCT 60.674 45.833 0.00 0.00 0.00 2.85
1794 1993 5.167845 GTCGATCTGCTTCTTCTTCTTCTT 58.832 41.667 0.00 0.00 0.00 2.52
1872 2077 1.867193 GATCGCGCGTTGCTAGCTAC 61.867 60.000 30.98 17.94 43.27 3.58
1873 2078 2.607668 ATCGCGCGTTGCTAGCTACA 62.608 55.000 30.98 5.67 43.27 2.74
1874 2079 2.441378 CGCGCGTTGCTAGCTACAA 61.441 57.895 24.19 6.02 43.27 2.41
1875 2080 1.752501 CGCGCGTTGCTAGCTACAAT 61.753 55.000 24.19 0.00 43.27 2.71
1876 2081 1.205657 GCGCGTTGCTAGCTACAATA 58.794 50.000 25.34 0.00 41.73 1.90
1974 2253 8.512138 ACGATTCTTTCTCGTTCCAATATTTTT 58.488 29.630 0.00 0.00 46.49 1.94
1999 2278 1.021968 GCGATTGTTTCCGGGCTTAT 58.978 50.000 0.00 0.00 0.00 1.73
2000 2279 2.215196 GCGATTGTTTCCGGGCTTATA 58.785 47.619 0.00 0.00 0.00 0.98
2001 2280 2.614983 GCGATTGTTTCCGGGCTTATAA 59.385 45.455 0.00 0.00 0.00 0.98
2002 2281 3.252458 GCGATTGTTTCCGGGCTTATAAT 59.748 43.478 0.00 0.00 0.00 1.28
2012 2291 9.059260 GTTTCCGGGCTTATAATTAATGAGTAA 57.941 33.333 0.00 0.00 0.00 2.24
2041 2320 1.509787 CGCGTGCGATTTGTTCCTG 60.510 57.895 8.89 0.00 42.83 3.86
2042 2321 1.574428 GCGTGCGATTTGTTCCTGT 59.426 52.632 0.00 0.00 0.00 4.00
2043 2322 0.452784 GCGTGCGATTTGTTCCTGTC 60.453 55.000 0.00 0.00 0.00 3.51
2083 2362 4.631131 TCAGTAGAACACACAGTGAATGG 58.369 43.478 7.81 0.00 36.96 3.16
2084 2363 3.187227 CAGTAGAACACACAGTGAATGGC 59.813 47.826 7.81 0.00 36.96 4.40
2085 2364 1.229428 AGAACACACAGTGAATGGCG 58.771 50.000 7.81 0.00 36.96 5.69
2119 2398 6.884187 TCTACTCGTGTAAAAATCTTGTTGC 58.116 36.000 0.00 0.00 0.00 4.17
2122 2401 3.002862 TCGTGTAAAAATCTTGTTGCGCT 59.997 39.130 9.73 0.00 0.00 5.92
2123 2402 3.357823 CGTGTAAAAATCTTGTTGCGCTC 59.642 43.478 9.73 2.14 0.00 5.03
2138 2417 2.877786 TGCGCTCTTCTTTTGTTGATCA 59.122 40.909 9.73 0.00 0.00 2.92
2152 2431 4.963878 ATCAGTTGGATCACCCGC 57.036 55.556 0.00 0.00 37.93 6.13
2180 2459 2.182842 GGTGCGATGGGTGATGCTC 61.183 63.158 0.00 0.00 0.00 4.26
2185 2464 1.442526 CGATGGGTGATGCTCTTGGC 61.443 60.000 0.00 0.00 42.22 4.52
2202 2481 6.514048 GCTCTTGGCAATGTATAGATTTCACC 60.514 42.308 0.00 0.00 41.35 4.02
2211 2490 7.849804 ATGTATAGATTTCACCTGTGTTGTC 57.150 36.000 0.00 0.00 0.00 3.18
2254 2533 5.079689 TGCATGACGGTGAAGTTCTTATA 57.920 39.130 4.17 0.00 0.00 0.98
2276 2555 3.941483 ACTCCAACTTCAAGAACACACTG 59.059 43.478 0.00 0.00 0.00 3.66
2294 2573 4.514577 CACGCACGGGGAGGCTAG 62.515 72.222 0.00 0.00 0.00 3.42
2420 2710 4.371624 TCATGGAACCAAGAGTGAATGT 57.628 40.909 0.00 0.00 0.00 2.71
2421 2711 4.728772 TCATGGAACCAAGAGTGAATGTT 58.271 39.130 0.00 0.00 0.00 2.71
2422 2712 4.520111 TCATGGAACCAAGAGTGAATGTTG 59.480 41.667 0.00 0.00 32.00 3.33
2428 2718 2.749621 CCAAGAGTGAATGTTGGCCTAC 59.250 50.000 10.70 10.70 44.62 3.18
2457 2747 2.224744 TGCCCTTTTGCTCTGTGTCATA 60.225 45.455 0.00 0.00 0.00 2.15
2468 2758 2.814336 TCTGTGTCATAGATCGGATCGG 59.186 50.000 12.08 6.67 0.00 4.18
2493 2783 1.228800 TGGCCAACCATGCATCACA 60.229 52.632 0.61 0.00 42.67 3.58
2494 2784 1.216178 GGCCAACCATGCATCACAC 59.784 57.895 0.00 0.00 35.26 3.82
2495 2785 1.534336 GGCCAACCATGCATCACACA 61.534 55.000 0.00 0.00 35.26 3.72
2533 2826 5.869888 CCGTATGTTGAAGCTTTCTACTCTT 59.130 40.000 0.00 0.00 36.56 2.85
2534 2827 7.033791 CCGTATGTTGAAGCTTTCTACTCTTA 58.966 38.462 0.00 0.00 36.56 2.10
2599 2892 2.441901 CCGCTCTCCTCCTGCTCT 60.442 66.667 0.00 0.00 0.00 4.09
2608 2901 1.620819 TCCTCCTGCTCTTGTTGTCTC 59.379 52.381 0.00 0.00 0.00 3.36
2715 3066 2.431942 CTGGGTGTACGTGTCGGC 60.432 66.667 0.00 0.00 0.00 5.54
2716 3067 3.927163 CTGGGTGTACGTGTCGGCC 62.927 68.421 0.00 0.00 0.00 6.13
2717 3068 3.688159 GGGTGTACGTGTCGGCCT 61.688 66.667 0.00 0.00 0.00 5.19
2718 3069 2.431942 GGTGTACGTGTCGGCCTG 60.432 66.667 0.00 0.00 0.00 4.85
2719 3070 2.431942 GTGTACGTGTCGGCCTGG 60.432 66.667 0.00 0.00 0.00 4.45
2744 3095 1.486310 GACCATAGTCATCCACCTGCA 59.514 52.381 0.00 0.00 42.99 4.41
2820 3171 1.536766 CCTACCTGTGTCGTCGTACAA 59.463 52.381 0.00 0.00 0.00 2.41
2825 3176 2.050168 TGTCGTCGTACAACCGCC 60.050 61.111 0.00 0.00 0.00 6.13
2826 3177 2.256461 GTCGTCGTACAACCGCCT 59.744 61.111 0.00 0.00 0.00 5.52
2857 3208 0.036164 AGGCATACCAGCGAACAACA 59.964 50.000 0.00 0.00 39.06 3.33
2888 3239 2.289320 CCATCTACTCTATGCCTGGCAC 60.289 54.545 25.99 0.00 43.04 5.01
2908 3259 1.355210 CGCGTCCAAACAAGCTGTT 59.645 52.632 0.00 0.00 43.41 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.551974 CACTCAACTGACATGGATTCTAAGATT 59.448 37.037 0.00 0.00 0.00 2.40
10 11 6.014242 AGTTCACTCAACTGACATGGATTCTA 60.014 38.462 0.00 0.00 44.28 2.10
11 12 4.897509 TCACTCAACTGACATGGATTCT 57.102 40.909 0.00 0.00 0.00 2.40
24 25 4.321378 GGTCTCTCTACCAGTTCACTCAAC 60.321 50.000 0.00 0.00 39.50 3.18
36 37 2.526432 TGTTGTGAGGGTCTCTCTACC 58.474 52.381 0.40 0.00 42.86 3.18
41 42 1.630878 GGGAATGTTGTGAGGGTCTCT 59.369 52.381 0.00 0.00 0.00 3.10
52 53 3.221771 TCACCACAAGAAGGGAATGTTG 58.778 45.455 0.00 0.00 0.00 3.33
53 54 3.490348 CTCACCACAAGAAGGGAATGTT 58.510 45.455 0.00 0.00 0.00 2.71
54 55 2.815589 GCTCACCACAAGAAGGGAATGT 60.816 50.000 0.00 0.00 0.00 2.71
55 56 1.815003 GCTCACCACAAGAAGGGAATG 59.185 52.381 0.00 0.00 0.00 2.67
56 57 1.707427 AGCTCACCACAAGAAGGGAAT 59.293 47.619 0.00 0.00 0.00 3.01
57 58 1.140312 AGCTCACCACAAGAAGGGAA 58.860 50.000 0.00 0.00 0.00 3.97
58 59 0.397941 CAGCTCACCACAAGAAGGGA 59.602 55.000 0.00 0.00 0.00 4.20
64 65 1.532868 GTAGTTGCAGCTCACCACAAG 59.467 52.381 6.25 0.00 0.00 3.16
181 182 6.015688 GCAACCTAGTACTATATGTGTGCCTA 60.016 42.308 2.33 0.00 0.00 3.93
184 185 5.844004 AGCAACCTAGTACTATATGTGTGC 58.156 41.667 2.33 12.21 0.00 4.57
189 192 6.761099 ATCGGAGCAACCTAGTACTATATG 57.239 41.667 2.33 4.45 36.31 1.78
193 196 3.067742 GCAATCGGAGCAACCTAGTACTA 59.932 47.826 1.89 1.89 36.31 1.82
207 210 1.001020 AAGTGGCATGGCAATCGGA 60.001 52.632 25.11 0.00 0.00 4.55
216 219 1.039233 GGTGGGATCCAAGTGGCATG 61.039 60.000 15.23 0.00 34.18 4.06
237 240 2.192664 TGCCTGAATTAAAGCACCGA 57.807 45.000 0.00 0.00 0.00 4.69
251 254 1.751927 GGAAGCATGAGGGTGCCTG 60.752 63.158 0.00 0.00 46.19 4.85
274 277 3.019564 GCCACCATGCTTGAAACTATCT 58.980 45.455 0.22 0.00 0.00 1.98
316 319 4.818534 AAGCATAACATTGCCATACTCG 57.181 40.909 0.00 0.00 43.83 4.18
459 501 2.403698 GCGCATGTTCGGTTTTGTAAAG 59.596 45.455 0.30 0.00 0.00 1.85
470 512 0.179181 AAGAGCAATGCGCATGTTCG 60.179 50.000 26.09 13.90 46.13 3.95
510 556 8.604184 ACTGCCTTGATAGATGATGAATAGATT 58.396 33.333 0.00 0.00 0.00 2.40
538 584 9.968870 ATTTTTAGTTACTTTTGGCGTTCATTA 57.031 25.926 0.00 0.00 0.00 1.90
541 587 7.481642 TGATTTTTAGTTACTTTTGGCGTTCA 58.518 30.769 0.00 0.00 0.00 3.18
567 613 5.945784 GCTACATGGCCTATGAATTTGGATA 59.054 40.000 18.41 1.76 39.21 2.59
582 628 2.517450 GCAGTCGTCGCTACATGGC 61.517 63.158 0.00 0.00 0.00 4.40
586 632 1.733041 GCTTGCAGTCGTCGCTACA 60.733 57.895 0.00 0.00 0.00 2.74
587 633 1.733041 TGCTTGCAGTCGTCGCTAC 60.733 57.895 0.00 0.00 0.00 3.58
599 645 2.175322 GCTCGCTTCAGTGCTTGC 59.825 61.111 0.00 0.00 0.00 4.01
637 684 2.546795 CCACAGTTCTTCGACTCTGCTT 60.547 50.000 0.00 0.00 0.00 3.91
641 688 3.256136 CCTAACCACAGTTCTTCGACTCT 59.744 47.826 0.00 0.00 37.42 3.24
648 695 2.054799 TGAGGCCTAACCACAGTTCTT 58.945 47.619 4.42 0.00 43.14 2.52
653 700 2.398588 TCCTATGAGGCCTAACCACAG 58.601 52.381 4.42 0.00 42.76 3.66
654 701 2.561209 TCCTATGAGGCCTAACCACA 57.439 50.000 4.42 0.00 43.72 4.17
655 702 2.972713 TGATCCTATGAGGCCTAACCAC 59.027 50.000 4.42 0.00 43.14 4.16
657 704 2.027653 GCTGATCCTATGAGGCCTAACC 60.028 54.545 4.42 0.00 34.61 2.85
674 751 0.940833 TTGATGTTTTCGTGCGCTGA 59.059 45.000 9.73 3.44 0.00 4.26
685 762 0.884704 AGCTGCGACGGTTGATGTTT 60.885 50.000 0.00 0.00 0.00 2.83
701 778 4.953667 TCGATCAGCAATTATCTTCAGCT 58.046 39.130 0.00 0.00 35.63 4.24
703 780 5.612059 CGCTTCGATCAGCAATTATCTTCAG 60.612 44.000 9.63 0.00 40.09 3.02
707 784 3.982475 TCGCTTCGATCAGCAATTATCT 58.018 40.909 9.63 0.00 40.09 1.98
736 813 2.734723 CGTCACCCGTGCTCTGTG 60.735 66.667 0.00 0.00 0.00 3.66
737 814 3.991051 CCGTCACCCGTGCTCTGT 61.991 66.667 0.00 0.00 33.66 3.41
738 815 4.742201 CCCGTCACCCGTGCTCTG 62.742 72.222 0.00 0.00 33.66 3.35
765 863 5.729510 CAAAAAGAAGGGTCAAAAGAACCA 58.270 37.500 2.00 0.00 38.62 3.67
794 909 4.081697 GTGGGGCAGCATGTTATTAAAAGT 60.082 41.667 0.00 0.00 39.31 2.66
797 912 3.435275 TGTGGGGCAGCATGTTATTAAA 58.565 40.909 0.00 0.00 39.31 1.52
821 936 2.530177 TCGCTCGATGTTTCACTGATC 58.470 47.619 0.00 0.00 0.00 2.92
871 987 5.415389 TCATGTGAAATGGGAATACACAGTG 59.585 40.000 0.00 0.00 43.02 3.66
973 1102 1.581447 CTCCGGCCTTTTTGTCTGC 59.419 57.895 0.00 0.00 0.00 4.26
978 1107 0.598065 CTCAACCTCCGGCCTTTTTG 59.402 55.000 0.00 0.00 0.00 2.44
995 1124 2.670414 CACGCTCTTCCATCTTTGACTC 59.330 50.000 0.00 0.00 0.00 3.36
1050 1182 5.381174 TTGATTCATGTGAAGGAAAGCTG 57.619 39.130 1.65 0.00 37.48 4.24
1070 1207 4.205792 GCTACCAATACGTACGTAGCTTTG 59.794 45.833 29.65 26.32 46.52 2.77
1103 1243 1.066454 GTTCGGGGTTTGGTTTGACTG 59.934 52.381 0.00 0.00 0.00 3.51
1111 1251 2.043980 CGGGATGTTCGGGGTTTGG 61.044 63.158 0.00 0.00 0.00 3.28
1767 1966 1.475441 GAAGAAGCAGATCGACGGCG 61.475 60.000 2.87 2.87 43.97 6.46
1792 1991 1.059264 GCAATCGAACGACGGAAGAAG 59.941 52.381 0.00 0.00 42.82 2.85
1793 1992 1.065358 GCAATCGAACGACGGAAGAA 58.935 50.000 0.00 0.00 42.82 2.52
1794 1993 0.242825 AGCAATCGAACGACGGAAGA 59.757 50.000 0.00 0.00 42.82 2.87
1872 2077 8.993121 ACCGAATTACTGCTAATGAATCTATTG 58.007 33.333 0.00 0.00 0.00 1.90
1873 2078 9.209175 GACCGAATTACTGCTAATGAATCTATT 57.791 33.333 0.00 0.00 0.00 1.73
1874 2079 8.589338 AGACCGAATTACTGCTAATGAATCTAT 58.411 33.333 0.00 0.00 0.00 1.98
1875 2080 7.952671 AGACCGAATTACTGCTAATGAATCTA 58.047 34.615 0.00 0.00 0.00 1.98
1876 2081 6.821388 AGACCGAATTACTGCTAATGAATCT 58.179 36.000 0.00 0.00 0.00 2.40
1974 2253 0.236187 CCGGAAACAATCGCGTCAAA 59.764 50.000 5.77 0.00 0.00 2.69
1999 2278 6.537301 CGGGTGCTTCTGTTACTCATTAATTA 59.463 38.462 0.00 0.00 0.00 1.40
2000 2279 5.354234 CGGGTGCTTCTGTTACTCATTAATT 59.646 40.000 0.00 0.00 0.00 1.40
2001 2280 4.876107 CGGGTGCTTCTGTTACTCATTAAT 59.124 41.667 0.00 0.00 0.00 1.40
2002 2281 4.250464 CGGGTGCTTCTGTTACTCATTAA 58.750 43.478 0.00 0.00 0.00 1.40
2119 2398 4.739046 ACTGATCAACAAAAGAAGAGCG 57.261 40.909 0.00 0.00 0.00 5.03
2138 2417 1.995376 AAAAAGCGGGTGATCCAACT 58.005 45.000 0.00 0.00 34.36 3.16
2166 2445 1.442526 GCCAAGAGCATCACCCATCG 61.443 60.000 0.00 0.00 42.97 3.84
2167 2446 2.412605 GCCAAGAGCATCACCCATC 58.587 57.895 0.00 0.00 42.97 3.51
2180 2459 6.319658 ACAGGTGAAATCTATACATTGCCAAG 59.680 38.462 0.00 0.00 0.00 3.61
2185 2464 8.044060 ACAACACAGGTGAAATCTATACATTG 57.956 34.615 6.40 0.00 0.00 2.82
2202 2481 4.898829 TGAACTTGAATGGACAACACAG 57.101 40.909 0.00 0.00 0.00 3.66
2211 2490 4.211794 GCATTGTTGGTTGAACTTGAATGG 59.788 41.667 0.00 0.00 35.37 3.16
2254 2533 3.941483 CAGTGTGTTCTTGAAGTTGGAGT 59.059 43.478 0.00 0.00 0.00 3.85
2420 2710 0.965439 GGCACAACATTGTAGGCCAA 59.035 50.000 17.04 0.00 44.90 4.52
2421 2711 0.897863 GGGCACAACATTGTAGGCCA 60.898 55.000 21.22 0.00 46.40 5.36
2422 2712 0.611896 AGGGCACAACATTGTAGGCC 60.612 55.000 21.46 21.46 44.84 5.19
2428 2718 2.137523 GAGCAAAAGGGCACAACATTG 58.862 47.619 0.00 0.00 35.83 2.82
2457 2747 1.319541 CACTACCACCGATCCGATCT 58.680 55.000 6.81 0.00 0.00 2.75
2493 2783 1.366366 CGGGAGGACGAGTTGTTGT 59.634 57.895 0.00 0.00 35.47 3.32
2494 2784 0.599558 TACGGGAGGACGAGTTGTTG 59.400 55.000 0.00 0.00 37.61 3.33
2495 2785 1.203994 CATACGGGAGGACGAGTTGTT 59.796 52.381 0.00 0.00 37.61 2.83
2533 2826 6.127101 TGTTATCGATCTGAAGAAGAGGGTA 58.873 40.000 0.00 0.00 38.67 3.69
2534 2827 4.956700 TGTTATCGATCTGAAGAAGAGGGT 59.043 41.667 0.00 0.00 38.67 4.34
2599 2892 3.071892 AGGATTGGGTTACGAGACAACAA 59.928 43.478 0.00 0.00 0.00 2.83
2608 2901 3.682858 CACAACAGTAGGATTGGGTTACG 59.317 47.826 0.00 0.00 0.00 3.18
2694 3040 1.798234 CGACACGTACACCCAGTCCA 61.798 60.000 0.00 0.00 0.00 4.02
2715 3066 0.620410 TGACTATGGTCCCACCCAGG 60.620 60.000 6.77 0.00 41.47 4.45
2716 3067 1.417890 GATGACTATGGTCCCACCCAG 59.582 57.143 6.77 0.00 41.47 4.45
2717 3068 1.507140 GATGACTATGGTCCCACCCA 58.493 55.000 6.77 0.00 41.47 4.51
2718 3069 0.765510 GGATGACTATGGTCCCACCC 59.234 60.000 6.77 0.00 41.47 4.61
2719 3070 1.141053 GTGGATGACTATGGTCCCACC 59.859 57.143 20.16 14.48 43.08 4.61
2728 3079 2.105477 GGACATGCAGGTGGATGACTAT 59.895 50.000 9.62 0.00 45.22 2.12
2744 3095 3.370953 GGATGAGGTTGCTACAAGGACAT 60.371 47.826 0.00 0.00 0.00 3.06
2857 3208 0.179045 GAGTAGATGGTTGCCCGCAT 60.179 55.000 0.00 0.00 0.00 4.73
2888 3239 2.978010 AGCTTGTTTGGACGCGGG 60.978 61.111 12.47 0.00 0.00 6.13
2898 3249 3.450578 CTGTTCATTGCAACAGCTTGTT 58.549 40.909 0.00 0.00 45.13 2.83
2908 3259 4.261322 GCTTTTCTCAGACTGTTCATTGCA 60.261 41.667 1.59 0.00 0.00 4.08
2922 3273 1.220529 CGACACTGCTGCTTTTCTCA 58.779 50.000 0.00 0.00 0.00 3.27


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.